scholarly journals Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model

ACS Nano ◽  
2017 ◽  
Vol 11 (12) ◽  
pp. 12426-12435 ◽  
Author(s):  
Rahul Sharma ◽  
John S. Schreck ◽  
Flavio Romano ◽  
Ard A. Louis ◽  
Jonathan P. K. Doye
Keyword(s):  
Coarse Grained ◽  
Dna Nanostructures ◽  
Coarse Grained Model

scholarly journals Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

2021 ◽  
Author(s):  
Yingnan Deng ◽  
Yuanhang Tan ◽  
Linghao Zhang ◽  
Chunyi Zhang ◽  
Xin Su
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Tumor Biomarker ◽  
Dna Nanostructures ◽  
Stimuli Responsive ◽  
Reaction Products ◽  
Coarse Grained Model ◽  
Sensitivity And Selectivity ◽  
Dna Nanotubes ◽  
Enzyme Recognition

Abstract The reactivity of DNA modifying enzymes on their natural nucleic acid substrates has been fully understood. However, their reactivity on self-assembled nanostructures of nucleic acid is complicated and unpredictable. Here, we employed the molecular dynamic simulation to forecast the reactivity of tumor biomarker enzymes on DNA nanotubes by coarse grained model. It is found that the enzyme accessibility and the potential energy of the reaction products co-determine the structural change of DNA nanotubes. The reactivity can be regulated by the position of enzyme recognition site. According to the simulation results, stimuli-responsive drug nanocarrier with superior sensitivity and selectivity was developed. Drug payloads released in cancer cells is 3.7~5.5-fold higher than that in normal cells. The DNA nanocarrier equipped with cancer-specific aptamer AS1411 is used to deliver doxorubicin (DOX) to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. This work provides new insights into the enzymatic reactivity of DNA nanostructures enriching the library of DNA-based reactions and heralding broad applications in nanomedicine.

scholarly journals 1P-074 Sampling enhancement for all-atom simulation using coarse-grained model(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S32
Author(s):  
Hiromitsu Shimoyama ◽  
Yasushige Yonezawa ◽  
Haruki Nakamura
Keyword(s):  
Annual Meeting ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Biophysical Society

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

scholarly journals A Novel Coarse-Grained Model to Study Liquid-Liquid Phase Separation of Disordered Proteins

2017 ◽  
Vol 112 (3) ◽  
pp. 200a
Author(s):  
Gregory L. Dignon ◽  
Wenwei Zheng ◽  
Robert Best ◽  
Jeetain Mittal
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Coarse Grained Model ◽  
Liquid Liquid Phase Separation

scholarly journals Molecular Dynamics Study of Ganglioside GM3/DPPC Membrane by Using Coarse-Grained Model

2016 ◽  
Vol 110 (3) ◽  
pp. 323a
Author(s):  
Kento Inoue ◽  
Eiji Ymamoto ◽  
Daisuke Takaiwa ◽  
Kenji Yasuoka ◽  
Masuhiro Mikami
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Ganglioside Gm3 ◽  
Coarse Grained Model

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

Sign in / Sign up

Export Citation Format

Share Document